rs10501031

chr11-25995267-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0665 in 152,218 control chromosomes in the GnomAD database, including 744 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.066 (744 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10107 AN: 152100 Hom.: 740 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.0335

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0665 AC: 10122 AN: 152218 Hom.: 744 Cov.: 33 AF XY: 0.0645 AC XY: 4803 AN XY: 74442

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.0372

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.0334

Gnomad4 SAS AF: 0.0489

Gnomad4 FIN AF: 0.00386

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0441 Hom.: 54

Bravo AF: 0.0720

Asia WGS AF: 0.0370 AC: 128 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.3
Dann	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10501031; hg19: chr11-26016814;